Publications

Abstract The gray mangrove [ Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina . We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188 bp long genome. The largest 32 scaffolds (22.4 Mb to 10.5 Mb) accounted for 98 % of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4 Kb to 1 Kb). We annotated 23,331 protein-coding genes using tissue-specific RNA-seq data, from which 13,312 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 92.3% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an F ST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation, and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.

Through sharing characteristics of chorus activity, especially in regions that are particularly data deficient, we can aim at a broader, global understanding of fish chorusing and consequently important spatiotemporal changes in habitat use by schooling fish. Here, we identify seasonal changes in fish chorusing activity using passive acoustic monitoring, in the central Red Sea mesophotic and adjacent shallow coral reef zones. For this study, recorders were placed in the mesophotic coral reef zone (70–80 m), and adjacent shallow reef sites (10 m), over 2 weeks during summer and winter seasons. A total of eleven choruses were identified and catalogued according to timing, location and acoustic characteristics of frequency and sound pressure levels. The presence of choruses in both deep and shallow reef sites is indicative of critical habitat for fish foraging, courtship, spawning, and/or migratory activity. All but two choruses were found to originate at or near the mesophotic sites. Four choruses unique to summer and winter (n=3 and 1 respectively) were most prevalent in soundscapes. Temperature and oxygen levels, measured to document conditions under which the choruses were present, showed little change across the mesophotic zone even between seasons, while daily fluctuation occurred in the adjacent shallow sites in both seasons.

An experiment was performed in order to analyze the effects of the increase in water temperature and CO2 partial pressure expected for the end of this century in a present phytoplankton community inhabiting the Arctic Ocean. We analyzed both factors acting independently and together, to test possible interactions between them. The arctic planktonic community was incubated under six different treatments combining three experimental temperatures (1, 6, and 10 ◦ C) with two different CO2 levels of 380 or 1000ppm, at the UNIS installations in Longyearbyen (Svalbard), in summer 2010. Under warmer temperatures, a decrease in chlorophyll a concentration, biovolume and primary production was found, together with a shift in community structure toward a dominance of smaller cells (nano-sized). Effects of increased pCO2 were more modest, and although interactions were weak, our results suggest antagonistic interactive effects amongst increased temperature and CO2 levels, as elevated CO2 compensated partially the decrease in phytoplankton biomass induced by temperature in some groups. Interactions between the two stressors were generally weak, but elevated CO2 was observed to lead to a steeper decline in primary production with warming. Our results also suggest that future increases in water temperature and pCO2 would lead to a decrease in the community chl a concentration and biomass in the Arctic phytoplankton communities examined, leading to communities dominated by smaller nano-phytoplankton groups, with important consequences for the flow of carbon and food web dynamics.

Abstract During the late cretaceous period several lineages of angiosperm plants transitioned from land to the sea by successfully adapting to life in salt water, forming the polyphyletic group of seagrasses. Today, four seagrass families inhabit coastal systems and are deeply intertwined with health and welfare of these ecosystems. Adaptation to the ocean environment included changes in the composition of plant cell walls and associated glycoproteins. We have asked the question whether or not there is a convergent and similar arabinogalactan-protein glycan repertoire in all seagrasses, given initial findings of arabinogalactan-proteins with unique features in the well-studied eelgrass, Zostera marina . We isolated and characterized arabinogalactan-proteins from seven species covering the four major seagrass families using carbohydrate analysis and glycan immunoassays, along with a bioinformatic search for relevant gene pathways in newly published seagrass genomes and transcriptomes. Glycan parts of all seagrass arabinogalactan-proteins shared a high proportion of 1,4-linked glucuronic acids and terminal 4- O -methyl glucuronic acid residues. Trait-based dendrograms generated to inform phylogenetic-relatedness showed there was no phylogenetic signal among seagrass families and arabinogalactan-protein features. Transcriptomic datasets from Cymodocea nodosa and Thalassia hemprichii growing under hypersaline conditions showed an upregulation of enzymes involved in 4 O -methylation and glucuronic acid transfer. We therefore conclude that environmental factors, especially salinity with higher monovalent ion concentration, influence seagrass arabinogalactan-proteins structure more intensely than phylogenetic history.

Abstract Mangroves have the capacity to sequester organic carbon (C org ) in their sediments permanently. However, the carbon budget of mangroves is also affected by the total alkalinity (TA) budget. Principally, TA emitted from carbonate sediment dissolution is a perennial sink of atmospheric CO 2 . The assessment of the TA budget of mangrove carbonate sediments in the Red Sea revealed a large TA emission of 403 ± 17 mmol m −2 d −1 , independent of light, seasons, or the presence of pneumatophores, compared to −36 ± 10 mmol m −2 d −1 in lagoon sediment. We estimate the TA emission from carbonate dissolution in Red Sea mangroves supported a CO 2 uptake of 345 ± 15 gC m −2 yr −1 , 23‐fold the C org burial rate of 15 gC m −2 yr −1 . The focus on C org burial in sediments may substantially underestimate the role of mangroves in CO 2 removal. Quantifying the role of mangroves in climate change mitigation requires carbonate dissolution to be included in assessments.

Sea turtles are an important part of marine and coastal ecosystems around the world. Yet, six of seven sea turtle species are endangered (IUCN, 2021). While they spend most of their lives at sea, female turtles use sandy beaches as nesting habitat, where they dig their nests in the sand to incubate for up to two months. A major challenge to sea turtles is the degradation of their nesting beaches due to anthropogenic climate-change effects, such as accelerated sea level rise (SLR) and anomalous storm activity. While it is still uncertain how sandy beaches will respond to SLR, beaches backed by hard structures cannot migrate landward, leading to ‘coastal squeeze’—the erosion and consequential narrowing of beaches. Increased storm activity may lead to persistently high water levels at nesting beaches, resulting in the flooding or even erosion of incubating nests. Moreover, beach erosion during storms can bury nests under excessive sand and limit beach access through the formation of scarps. Nature-based solutions—for example in the form of turtle-friendly design of beaches along new land reclamations or by adding coastal vegetation or reefs to limit runup and reduce erosion on existing beaches—may offer promising opportunities to preserve and even expand global habitats for turtle nesting.

The recurrent lack of isolation by distance reported at regional scale in seagrass species was recently suggested to stem from stochastic events of large-scale dispersal. We explored the usefulness of phylogenetic information contained in microsatellite loci to test this hypothesis by using the Genetic Diversity Spectrum (GDS) on databases containing, respectively, 7 and 9 microsatellites genotypes for 1541 sampling units of Posidonia oceanica and 1647 of Cymodocea nodosa. The simultaneous increase of microsatellite and geographic distances that emerges reveals a coherent pattern of isolation by distance in contrast to the chaotic pattern previously described using allele frequencies, in particular, for the long-lived P. oceanica. These results suggest that the lack of isolation by distance, rather than the resulting from rare events of large-scale dispersal, reflects at least for some species a stronger influence of mutation over migration at the scale of the distribution range. The global distribution of genetic polymorphism may, therefore, result predominantly from ancient events of step-by-step (re)colonization followed by local recruitment and clonal growth, rather than contemporary gene flow. The analysis of GDS appears useful to unravel the evolutionary forces influencing the dynamics and evolution at distinct temporal and spatial scales by accounting for phylogenetic information borne by microsatellites, under an appropriate mutation model. This finding adds nuance to the generalization of the influence of large-scale dispersal on the dynamics of seagrasses.

Abstract The deep sea, the largest compartment of the ocean, is an essential component of the Earth system, but the functional exploration of its microbial communities lags far behind that of other marine realms. Here we analyze 58 bathypelagic microbial metagenomes from the Atlantic, Indian, and Pacific Oceans in an unprecedented sampling effort from the Malaspina Global Expedition, to resolve the metabolic architecture of the deep ocean microbiome. The Malaspina Deep-Sea Gene Collection, 71% of which consists of novel genes, reveals a strong dichotomy between the functional traits of free-living and particle-attached microorganisms, and shows relatively patchy composition challenging the paradigm of a uniform dark ocean ecosystem. Metagenome Assembled Genomes uncovered 11 potential new phyla, establishing references for deep ocean microbial taxa, and revealed mixotrophy to be a widespread trophic strategy in the deep ocean. These results expand our understanding of the functional diversity, metabolic versatility, and carbon cycling in the largest ecosystem on Earth. One Sentence Summary A whole community genomic survey of the deep microbiome sheds light on the microbial and functional diversity of the dark ocean.